Researchers have hijacked a defense system normally used by bacteria to fend off viral infections and redirected it against the human papillomavirus (HPV), the virus that causes cervical, head and neck, and other cancers.
Using the genome editing tool known as CRISPR, the Duke University researchers were able to selectively destroy two viral genes responsible for the growth and survival of cervical carcinoma cells, causing the cancer cells to self-destruct.
The findings, published in the Journal of Virology, give credence to an approach only recently attempted in mammalian cells, and could pave the way toward antiviral strategies targeted against other DNA-based viruses like hepatitis B and herpes simplex.
"Because this approach is only going after viral genes, there should be no off-target effects on normal cells," said Bryan R. Cullen, Ph.D., senior study author and professor of molecular genetics and microbiology at Duke University School of Medicine. "You can think of this as targeting a missile that will destroy a certain target. You put in a code that tells the missile exactly what to hit, and it will only hit that, and it won't hit anything else because it doesn't have the code for another target."
In this study, Cullen decided to target the human papillomavirus (HPV), which causes almost all cervical cancers and about half of head and neck cancers. Specifically, he and his colleagues went after the viral genes E6 and E7, two "oncogenes" that block the host's own efforts to keep cancer cells at bay.
To run CRISPR against the virus, the researchers needed two ingredients. First, they needed the target code for E6 or E7, consisting of a short strip of RNA sequence, the chemical cousin of DNA. To this "guide RNA" they added the Cas9 protein, which would cut any DNA that could line up and bind to that RNA sequence.
The carcinoma cells that received the anti-HPV guide RNA/Cas9 combination immediately stopped growing. In contrast, cells that had received a control virus, containing a random guide RNA sequence, continued on their path to immortality. The researchers then dug down to the molecular level to investigate the consequences of destroying E6 or E7 in cancer cells. E6 normally blocks a protein called p53, known as the guardian of the genome because it can turn on suicide pathways in the cell when it senses that something has gone awry. In this study, targeting E6 enabled p53 to resume its normal function, spurring death of the cancer cell.
E7 works in a similar way, blocking another protein called retinoblastoma or Rb that can trigger growth arrest and senescence, another form of cell death. As expected, the researchers found that targeting E7 also set this second "tumor suppressor" back in motion.
"As soon as you turn off E6 or E7, the host defense mechanisms are allowed to come back on again, because they have been there this whole time, but they have been turned off by HPV," Cullen said. "What happens is the cell immediately commits suicide."
Cullen and his colleagues are now working on developing a different viral vector, based on the adeno-associated virus, to deliver their CRISPR cargo into cancer cells. Once they are happy with their delivery system, they will begin to test this approach in animal models.
"What we would hope to see in an HPV-induced cancer is rapid induction of tumor necrosis caused by loss of E6 or E7," Cullen said. "This method has the potential to be a single hit treatment that will dramatically reduce tumor load without having any effect on normal cells."
The researchers are also targeting other viruses that use DNA as their genetic material, including the hepatitis B virus and herpes simplex virus.
Reference: "Inactivation of the human papillomavirus E6 or E7 gene in cervical carcinoma cells using a bacterial CRISPR/Cas RNA-guided endonuclease," Edward M. Kennedy, Anand V. R. Kornepati, Michael Goldstein, Hal P. Bogerd, Brigid C. Poling, Adam W. Whisnant, Michael B. Kastan and Bryan R. Cullen.Journal of Virology, August 6, 2014. DOI 10.1128/JVI.01879-14.
Without a question, we are living in an urban era. More people now live in cities than anywhere else on the planet and I’ve repeatedly argued that cities are our most important economic engine. As a result of these shifts, we’re seeing megacities at a scale the world has never seen before.
CRISPR-PLANT Database - http://www.genome.arizona.edu/crispr "enables the plant research community to access genome-wide predictions of specific gRNAs, and facilitate the application of CRISPR-Cas9 mediated genome editing in model plants and major agricultural crops".
Professor of Genetics Scott Williams, PhD, of the Institute for Quantitative Biomedical Sciences (iQBS) at Dartmouth’s Geisel School of Medicine, has made two novel discoveries: first, a person can have several DNA mutations in parts of their body, with their original DNA in the rest—resulting in several different genotypes in one individual—and second, some of the same genetic mutations occur in unrelated people. We think of each person’s DNA as unique, so if an individual can have more than one genotype, this may alter our very concept of what it means to be a human, and impact how we think about using forensic or criminal DNA analysis, paternity testing, prenatal testing, or genetic screening for breast cancer risk, for example. Williams’ surprising results indicate that genetic mutations do not always happen purely at random, as scientists have previously thought. His work, done in collaboration with Professor of Genetics Jason Moore, PhD, and colleagues at Vanderbilt University, was published in PLOS Genetics journal.
Genetic mutations can occur in the cells that are passed on from parent to child and may cause birth defects. Other genetic mutations occur after an egg is fertilized, throughout childhood or adult life, after people are exposed to sunlight, radiation, carcinogenic chemicals, viruses, or other items that can damage DNA. These later or “somatic” mutations do not affect sperm or egg cells, so they are not inherited from parents or passed down to children. Somatic mutations can cause cancer or other diseases, but do not always do so. However, if the mutated cell continues to divide, the person can develop tissue, or a part thereof, with a different DNA sequence from the rest of his or her body.
“We are in reality diverse beings in that a single person is genetically not a single entity—to be philosophical in ways I do not yet understand—what does it mean to be a person if we are variable within?” says Williams, the study’s senior author, and founding Director of the Center for Integrative Biomedical Sciences in iQBS. “What makes you a person? Is it your memory? Your genes?” He continues, “We have always thought, ‘your genome is your genome.’ The data suggest that it is not completely true.”
In the past, it was always thought that each person contains only one DNA sequence (genetic constitution). Only recently, with the computational power of advanced genetic analysis tools that examine all the genes in one individual, have scientists been able to systematically look for this somatic variation. “This study is an example of the type of biomedical research project that is made possible by bringing together interdisciplinary teams of scientists with expertise in the biological, computational and statistical sciences.” says Jason Moore, Director of the iQBS, who is also Associate Director for Bioinformatics at the Cancer Center, Third Century Professor, and Professor of Community and Family Medicine at Geisel.
Having multiple genotypes from mutations within one’s own body is somewhat analogous to chimerism, a condition in which one person has cells inside his or her body that originated from another person (i.e., following an organ or blood donation; or sometimes a mother and child—or twins—exchange DNA during pregnancy. Also, occasionally a person finds out that, prior to birth, he or she had a twin who did not survive, whose genetic material is still contained within their own body). Chimerism has resulted in some famous DNA cases: one in which a mother had genetic testing that “proved” that she was unrelated to two of her three biological sons.
We describe a transcription activator-like effector (TALE)-based strategy, termed “TALEColor,” for labeling specific repetitive DNA sequences in human chromosomes. We designed TALEs for the human telomeric repeat and fused them with any of numerous fluorescent proteins (FPs). Expression of these TALE–telomere–FP fusion proteins in human osteosarcoma's (U2OS) cells resulted in bright signals coincident with telomeres. We also designed TALEs for centromeric sequences unique to certain chromosomes, enabling us to localize specific human chromosomes in live cells. Meanwhile we generated TALE–FPs in vitro and used them as probes to detect telomeres in fixed cells. Using human cells with different average telomere lengths, we found that the TALEColor signals correlated positively with telomere length. In addition, suspension cells were followed by imaging flow cytometry to resolve cell populations with differing telomere lengths. These methods may have significant potential both for basic chromosome and genome research as well as in clinical applications.
Here, we report, for the first time, targeted mutagenesis in Zea mays using TALENs and the CRISPR/Cas system. We designed five TALENs targeting 4 genes, namely ZmPDS, ZmIPK1A, ZmIPK, ZmMRP4, and obtained targeting efficiencies of up to 23.1% in protoplasts, and about 13.3% to 39.1% of the transgenic plants were somatic mutations. Also, we constructed two gRNAs targeting the ZmIPK gene in maize protoplasts, at frequencies of 16.4% and 19.1%, respectively. In addition the CRISPR/Cas system induced targeted mutations in Zea mays protoplasts with efficiencies (13.1%) similar to those obtained with TALENs (9.1%). Our results show that both TALENs and the CRISPR/Cas system can be used for genome modification in maize.
In reverse genetics, a gene’s function is elucidated through targeted modifications in the coding region or associated DNA cis-regulatory elements. To this purpose, recently developed customizable transcription activator-like effector nucleases (TALENs) have proven an invaluable tool, allowing introduction of double-strand breaks at predetermined sites in the genome. Here we describe a practical and efficient method for the targeted genome engineering in Drosophila. We demonstrate TALEN-mediated targeted gene integration and efficient identification of mutant flies using a traceable marker phenotype. Furthermore, we developed an easy TALEN assembly (easyT) method relying on simultaneous reactions of DNA Bae I digestion and ligation, enabling construction of complete TALENs from a monomer unit library in a single day. Taken together, our strategy with easyT and TALEN-plasmid microinjection simplifies mutant generation and enables isolation of desired mutant fly lines in the F1 generation.
IRRI and PhilRice officials visit the Golden Rice field site that was vandalized... A crowd of 300 had stormed the Department of Agriculture (DA) Regional Field Unit 5's (RFU5) Bicol Experiment Station, overwhelming the police and guards, and vandalizing the research plots of Golden Rice...
Regional Executive Diretor Bragas said that they were taken by surprise. They had assembled DA officials and staff in the office, waiting for the group to come in and sit down for a peaceful dialogue. Instead, the militants poured into the compound, overwhelmed the police and village security, broke down a section of the fence surrounding the research area, and entered, uprooted, and trampled the crop.
The officials shared that there were farmers in the group, but they just watched and stayed on the sidelines. Local customs and traditions dictate that the destruction of a living field brings bad fortune – Bicolanos refer to it as "Bosung". Those who entered the field to vandalize were mostly young men and some covered their faces.
The local officials and the Institutional Biosafety Committee (IBC) recounted that the rallyists had been assembled in Legazpi City the day before, and brought overnight to Naga City in a convoy of about a dozen jeepneys. In Naga City they had been housed in local hotels. It was reported that the group included foreigners.
We’ve come a long way since scientists cloned the first adult mammal, a sheep named Dolly, in 1996. Now, you can pay to have your own dog duplicated using the same technique scientists used to make Dolly. But there’s a catch (aside, of course, from the whole ethical dilemma of incubating your recently deceased pet’s cells inside a random pup): It costs around $US100,000, and there’s only one lab in the world that does it. In South Korea.
To clone a dog, scientists at the Sooam Biotech Research Foundation laboratory do exactly what researchers did to make Dolly. First, they take a few cells from your pet and reprogram them to stop growing — effectively putting their DNA to sleep. Then, using a tiny straw-like device, they suck up the dormant cell and inject it inside another dog cell that’s been emptied of its nucleus, or command center. Then the scientists zap the new cell with electricity, coaxing the two parts to fuse into one cell. Once they make sure the new cell “works,” meaning it can divide and develop on its own, the scientists implant it inside a surrogate mama pup. In a few months, if all goes well, the surrogate dog will give birth to a puppy that looks just like yours.
The new animal won’t be absolutely identical, of course. Missing all the memories of the old animal, for starters. “When thinking of cloning, try to think of an identical twin,” Sooam biologist Insung Hwang explains. “The dog will not be 100% the same — the spots on a Dalmatian clone will be different, for example — but for breeds without such characteristics it will be very hard to tell them apart.”
The lab that oversees the procedure isn’t without controversy, however. Eight years after winning international acclaim for cloning the world’s first dog in 2005, Sooam founder and veterinarian by training Woo Suk Hwang was publically disgraced for falsifying research on human embryo cloning. Hwang (no relation to Insung Hwang) was expelled from Seoul National University, where he did the research, and is still facing criminal charges.
Despite the public outcry, Hwang’s supporters managed to gather more than $US3.5 million to help him start Sooam in 2006. Since then, the lab has cloned more than 400 dogs, mostly pets, reports Nature. In the past few years, Sooam researchers have picked up their pace, producing about 15 puppies a month.
Beyond Dog Cloning:
Some scientists want to use Sooam’s cloning technique to replicate far more than people’s deceased pups. Geneticist George Church and Sooam biologist Insung Hwang, for example, are exploring the possibility of bringing long-extinct animals back to life using samples of their DNA. Church and Hwang are part of a team of researchers who recently autopsied the body of a woolly mammoth who lived about 40,000 years ago and whose blood was surprisingly well preserved, along with her body, in Siberia. The autopsy is featured in detail in a recent Smithsonian documentary called “How To Clone A Woolly Mammoth.”
Using 17 genomes, researchers were unable to find rare protein-altering variants significantly associated with extreme longevity, according to a study published November 12, 2014 in the open-access journal PLOS ONE by Hinco Gierman from Stanford University and colleagues.
Supercentenarians are the world’s oldest people, living beyond 110 years of age. Seventy-four are alive worldwide; 22 live in the U.S. The authors of this study performed whole-genome sequencing on 17 supercentenarians to explore the genetic basis underlying extreme human longevity.
In my quest to learn about genetically modified foods and our food supply, many things have surprised me. Some of them may seem apparent and obvious, but as a city-dweller, I was unaware of numerous aspects of our food. I find comfort in the fact that many individuals that I share these gems with are equally surprised, leading me to believe that you may find some items as interesting as I do.
1) The vast majority of fruits and vegetables are not transgenics... Every time I picked up a fruit in the supermarket that was particularly large, I thought to myself “huh… that’s got to be a GMO”. You know those grapes the size of tennis balls that squirt juice everywhere when you bite into them? Every time I ate one, I’d close my eyes and thank the mysterious GMO gods for that sweet delicious nectar. Little did I know that none of these fruits was a GMO...
2) Organic food production uses pesticides. I had always believed that by definition, organic food production did not use pesticides. Not only that, but some of the pesticides used are more toxic than those applied in conventional farming. The difference is that the pesticides used in organic farming are not synthetic, yet they are not necessarily better...
3) Many plant traits are developed using mutagenesis. And can be labeled “organic”. Mutagenesis is the use of radioactivity or chemicals to create random mutations... More than 2000 foods have been created by mutagenesis, including the durum wheat used to make fine Italian pasta... and even ruby red grapefruits... Imagine that!! The delicious, organic grapefruit from my farmers’ market was developed using radiation to randomly create mutations, and somehow that’s less scary than a GMO. Why the organic food movement isn’t fighting to label the mutant ruby reds seems hypocritical...
4) There’s lot of peer reviewed research on GMOs, both publically and privately funded. I mean a LOT. Searching for the term MON810 in PubMed (a database hosted by the NIH), finds over 150 hits. That’s 150+ studies that have looked into some aspect, such as identification or safety, on a single[!] seed/trait... the most common misconception about GMOs is that there are few independent studies. In an attempt to address this misconception...
5) Types of traits used to generate GMOs are selected to improve farming conditions. There aren’t many GM crops in which the trait introduced was selected because it would make me want to buy it in the grocery store... at the moment, most crops are designed to help consumers indirectly by benefitting farmers, such as Bt crops that cut down on the amount of pesticides sprayed to fight worms, or glyphosate-resistant crops, which help farmers reduce the use of toxic chemicals to fight weeds. We, the consumers, see the benefits of these traits because reduced farming costs equate to savings at the grocery store...
6) The amount of misinformation and the distrust surrounding GMOs is staggering. And depressing. It ranges from the subtle, in which statements are taken out of context or the complete findings of a paper are not discussed, to outright lies... GMO critics often peddle white lies as well as downright deceptive (and dangerous) statements such as claiming that GM insulin poses a health risk...
Dr Neil DeGrasse Tyson said it best... “If your objection to GMOs is the morality of selling non-perennial seed stocks, then focus on that. If your objection to GMOs is the monopolistic conduct of agribusiness, then focus on that. But to paint the entire concept of GMO with these particular issues is to blind yourself to the underlying truth of what humans have been doing—and will continue to do—to nature so that it best serves our survival...
I was surprised at how many people distrust GMOs because of their belief that Monsanto is an ‘evil’ company. That’s not a good reason for distrusting a technology with broad applications. It’s like saying that you don’t trust computers because of Microsoft. But conventional and even organic food growers buy Monsanto seeds too, and Monsanto doesn’t have a monopoly on GM technology...
7) Transgenic seeds are not sterile. I was certain that transgenic seeds could not be replanted, even if a farmer wanted to. I was dead wrong... the seed is not sterile or unviable...
8) Peer review often may not mean very much. Papers should be evaluated based on their quality...
9) The world’s most reputable scientific organizations have evaluated the data on the safety of GMOs. That’s right, there’s a scientific consensus on the topic of GMO safety... right now it’s very strong and consistent: GMOs are safe...
In 1992, a pair of scientists had a brain wave: How about inserting genes into rice that would boost its vitamin A content? By doing so, tens of millions of poor people who depend on rice as a staple could get a vital nutrient, potentially averting hundreds of thousands of cases of blindness each year. The idea for what came to be called “golden rice” — named for its bright yellow hue — was proclaimed as a defining moment for genetically modified food.
Backers said the initiative ushered in an era when GM crops would start to help the poor and malnourished... “It’s a humanitarian project,” said one of the co-inventors of golden rice, Ingo Potrykus, professor emeritus at the Swiss Federal Institute of Technology (ETH)...
Yet the rice is still a long way from appearing in food bowls — 2016 has become the latest date sketched for commercialization, provided the novel product gets the go-ahead... First, it took scientists years to find and insert two genes that modified the metabolic pathway in rice to boost levels of beta carotene, the precursor to vitamin A.
After that came the biosafety phase, to see if the rice was safe for health and the environment — and whether beta carotene levels in lab plants were replicated in field trials in different soils and climates. There were also “bioefficacy” experiments to see whether the rice did indeed overcome vitamin deficiency, and whether volunteers found the taste acceptable...
“We have been working on this for a long time, and we would like to have this process completed as soon as possible”... But “it depends on the regulatory authorities. That is not under our control.”
Coming on the heels of golden rice is the “superbanana” developed by the Queensland University of Technology in Australia with the help of the Bill and Melinda Gates Foundation. It too is genetically designed to be enriched with beta carotene... Project leader James Dale said the so-called cooking bananas that are grown as the staple food in East Africa are low in vitamin A and iron. “Good science can make a massive difference here,” he said...
It took 15 years of enclosed research in the lab for British scientists this year to decide to seek permission for field trials of a plant called false flax... Engineered to create omega-3 fat, the plant could be used as feed in fish farming. It would spare the world’s fish stocks, which provide food pellets for captive salmon, trout and other high-value species...
Andrea Sonnino, chief of the Research and Extension Unit at the U.N.’s Food and Agriculture Organization (FAO), said ensuring food security and a decent diet are very complex. GM crops have a part to play in the solution, but not exclusively so. “We have to go with a set of possible answers to problems that in many cases are technological and in many cases are not — they are social, economic and so on,” he said. “We have to work in different ways, and not only on the technological front.”
Genome Editing with CRISPR Systems Genetic Engineering News CRISPR endonucleases have been used in a recent flood of literature due to their elegant and simple mode of RNA-guided gene targeting and ability to operate via protocols developed...
Epigenetic regulation of gene expression involves, besides DNA and histone modifications, the relative positioning of DNA sequences within the nucleus. To trace specific DNA sequences in living cells, we used programmable sequence-specific DNA binding of designer transcription activator-like effectors (dTALEs). We designed a recombinant dTALE (msTALE) with variable repeat domains to specifically bind a 19-bp target sequence of major satellite DNA. The msTALE was fused with green fluorescent protein (GFP) and stably expressed in mouse embryonic stem cells. Hybridization with a major satellite probe (3D-fluorescent in situ hybridization) and co-staining for known cellular structures confirmed in vivo binding of the GFP-msTALE to major satellite DNA present at nuclear chromocenters. Dual tracing of major satellite DNA and the replication machinery throughout S-phase showed co-localization during mid to late S-phase, directly demonstrating the late replication timing of major satellite DNA. Fluorescence bleaching experiments indicated a relatively stable but still dynamic binding, with mean residence times in the range of minutes. Fluorescently labeled dTALEs open new perspectives to target and trace DNA sequences and to monitor dynamic changes in subnuclear positioning as well as interactions with functional nuclear structures during cell cycle progression and cellular differentiation.
Despite their growing popularity, little is known about binding site parameters that influence TALE-mediated gene activation in mammalian cells. We demonstrate that TALE activators modulate gene expression in mammalian cells in a position- and strand-dependent manner. To study the effects of binding site location, we engineered TALEs customized to recognize specific DNA sequences located in either the promoter or the transcribed region of reporter genes. We found that TALE activators robustly activated reporter genes when their binding sites were located within the promoter region. In contrast, TALE activators inhibited the expression of reporter genes when their binding sites were located on the sense strand of the transcribed region. Notably, this repression was independent of the effector domain utilized, suggesting a simple blockage mechanism. We conclude that TALE activators in mammalian cells regulate genes in a position- and strand-dependent manner that is substantially different from gene activation by native TALEs in plants. These findings have implications for optimizing the design of custom TALEs for genetic manipulation in mammalian cells.
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